NetLogo User Community Models

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# OVERVIEW

This simulation model was designed to simulate population dynamics and the evolution of the **boundary-crossing response** in a landscape context. The **boundary-crossing response** is the tendency to cross habitat boundaries, i.e. when a dispersing individual encounters a habitat boundary, does it turn back into habitat, or cross into non-habitat (also called 'matrix')?

The landscape context is determined by the values for four landscape attributes:

1. **habitat amount**: the proportion of the grid cells in habitat; smaller values mean less habitat

1. **habitat fragmentation**: the level of patchiness of habitat, for a given habitat amount, modeled as the Hurst exponent of the midpoint displacement algorithm used to assign locations of habitat and matrix cells (Saupe 1988); smaller values produce more fragmented habitat

1. **disturbance frequency**: mean number of generations until local population extinction (i.e. death of all individuals in a given habitat patch), for a Poisson distribution; smaller values indicate more frequent disturbance

Because the boundary-crossing response likely evolves along with other dispersal characteristics, the model includes three additional dispersal characteristics. All four dispersal characteristics can evolve, because each is modeled as a heritable trait:

1. **probability of boundary crossing**: probability that the individual will cross from habitat to matrix, when it encounters a boundary

1. **path shape in matrix**: correlation in movement direction between successive movement steps originating in matrix, modeled as the concentration parameter for a wrapped Cauchy distribution with a mean of zero

1. **path shape in habitat**: correlation in movement direction between successive movement steps originating in habitat, modeled as the concentration parameter for a wrapped Cauchy distribution with a mean of zero

Note that we use **habitat cell** and **matrix cell** when referring to a single habitat or matrix cell, respectively. **Habitat patch** refers to a contiguous group of habitat cells surrounded by matrix, where habitat cells are grouped based on a Moore (8-neighbor) neighborhood rule.

For full details, see Martin and Fahrig (2015).

##HOW TO CITE

We ask that you cite both our peer-reviewed paper and the NetLogo software:

A **simulation run** is initiated by creating an artificial landscape and populating it with individuals, each with a random value for its initial heritable probability of boundary crossing, dispersal propensity, path shape in matrix, and path shape in habitat. A simulation run continues for a user-specified number of generations, or until the population goes extinct.

Each generation involves:

1. **habitat disturbance**, resulting in some local population extinctions

1. **dispersal**, i.e. movement of individuals from their birth place, resulting in either dispersal mortality or settlement in a new location

# MODEL INTERFACE

## MAIN ACTIONS* **set-up**: prepares for a simulation run; must be pressed prior to the model run

* **run-model**: runs a single simulation run, for a user-defined number of generations

##OUTPUT CONTROLS

* **save-output**: ON = model output is saved to a space-delimited plain text file, adding a row to the file (specified by **output-file-name**) in each simulated generation (see **MODEL OUTPUT** below); OFF = no data are saved

* **save-final-generation**: ON = data for the landscape and population after the final generation are saved to space-delimited plain text files, at the end of a simulation run (see **MODEL OUTPUT** below); OFF = no data are saved

* **file-directory**: path to a directory and folder where data can be saved

* **output-file-name**: name of the text file where model output is saved (for **save-output**)

* **run-id**: numerical id for a simulation run; you must use a unique value for each simulation run you save to a given folder

##MODEL PARAMETERSThe set of user-defined model parameters.

_The user must pay attention to the accepted range of values for each parameter (defined in brackets, below). If any parameter value is outside its accepted range, the model run will stop, and a message identifying the problem parameter(s) will be printed to the 'Command Center'._

###ConstantsThese parameter values remain constant, at the user-defined values, for each simulation run:

* **generations**: number of simulated generations (>=1)

* **lambda**: variable in the equation used to calculate the mean number of offspring produced by each adult inhabiting a habitat cell (Hassell 1975) (>=1)

* **carring-capacity**: variable in the equation used to calculate the mean number of offspring produced by each adult inhabiting a habitat cell (Hassell 1975); also determines whether a dispersing individual settles or continues moving (it can only settle if the habitat cell is below capacity) (>=1)

* **competition-type**: variable in the equation used to calculate the mean number of offspring produced by each adult inhabiting a habitat cell (Hassell 1975); 1 = contest competition, >1 = scramble competition (>= 1)

* **mutation-rate**: probability of mutation for a given dispersal characteristic (0 - 1)

* **mutation-increment**: change in the value of a dispersal characteristic, when mutation occurs (0 - 0.5)

###Landscape attributesFor these parameters, the model randomly selects a value for each landscape attribute in each simulation run, based on the user-defined ranges: